You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Human Metabolome Database.
Record Information
Version3.6
Creation Date2013-06-15 18:25:05 UTC
Update Date2017-03-02 22:05:17 UTC
HMDB IDHMDB60639
Secondary Accession NumbersNone
Metabolite Identification
Common NameGemcitabine diphosphate
DescriptionGemcitabine diphosphate is a metabolite of gemcitabine. Gemcitabine is a nucleoside analog used as chemotherapy. It is marketed as Gemzar by Eli Lilly and Company. (Wikipedia)
Structure
Thumb
SynonymsNot Available
Chemical FormulaC9H13F2N3O10P2
Average Molecular Weight423.158
Monoisotopic Molecular Weight423.004423085
IUPAC Name[({[(2R,3R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-4,4-difluoro-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid
Traditional Name{[(2R,3R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-4,4-difluoro-3-hydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxyphosphonic acid
CAS Registry NumberNot Available
SMILES
NC1=NC(=O)N(C=C1)[C@@H]1O[C@H](COP(O)(=O)OP(O)(O)=O)[C@@H](O)C1(F)F
InChI Identifier
InChI=1S/C9H13F2N3O10P2/c10-9(11)6(15)4(3-22-26(20,21)24-25(17,18)19)23-7(9)14-2-1-5(12)13-8(14)16/h1-2,4,6-7,15H,3H2,(H,20,21)(H2,12,13,16)(H2,17,18,19)/t4-,6-,7-/m1/s1
InChI KeyFRQISCZGNNXEMD-QPPQHZFASA-N
Chemical Taxonomy
DescriptionThis compound belongs to the class of chemical entities known as organic pyrophosphates. These are organic compounds containing the pyrophosphate oxoanion, with the structure OP([O-])(=O)OP(O)([O-])=O.
KingdomChemical entities
Super ClassOrganic compounds
ClassOrganic oxygen compounds
Sub ClassOrganic oxoanionic compounds
Direct ParentOrganic pyrophosphates
Alternative Parents
Substituents
  • Organic pyrophosphate
  • Aminopyrimidine
  • Pyrimidone
  • Monoalkyl phosphate
  • Hydropyrimidine
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Primary aromatic amine
  • Pyrimidine
  • Alkyl phosphate
  • Imidolactam
  • Tetrahydrofuran
  • Heteroaromatic compound
  • Secondary alcohol
  • Fluorohydrin
  • Halohydrin
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Organic oxide
  • Organonitrogen compound
  • Organofluoride
  • Organopnictogen compound
  • Alkyl fluoride
  • Organohalogen compound
  • Alcohol
  • Organooxygen compound
  • Hydrocarbon derivative
  • Alkyl halide
  • Primary amine
  • Amine
  • Organic nitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
StatusExpected but not Quantified
Origin
  • Drug metabolite
Biofunction
  • Waste products
ApplicationNot Available
Cellular locations
  • Cytoplasm
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility14.1 mg/mLALOGPS
logP-0.13ALOGPS
logP-2ChemAxon
logS-1.5ALOGPS
pKa (Strongest Acidic)1.77ChemAxon
pKa (Strongest Basic)-0.68ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count10ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area201.44 Å2ChemAxon
Rotatable Bond Count6ChemAxon
Refractivity75 m3·mol-1ChemAxon
Polarizability30.87 Å3ChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
SpectraNot Available
Biological Properties
Cellular Locations
  • Cytoplasm
Biofluid Locations
  • Blood
  • Urine
Tissue Location
  • Kidney
  • Liver
Pathways
NameSMPDB LinkKEGG Link
Gemcitabine Metabolism PathwaySMP00603Not Available
Gemcitabine PathwaySMP00446Not Available
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot ApplicableNot AvailableNot AvailableNormal
  • Not Applicable
details
UrineExpected but not QuantifiedNot ApplicableNot AvailableNot AvailableNormal
  • Not Applicable
details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
DrugBank Metabolite IDDBMET00858
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
NuGOwiki LinkHMDB60639
Metagene LinkHMDB60639
METLIN IDNot Available
PubChem Compound6420157
PDB IDNot Available
ChEBI IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available